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Species are going extinct 1,000 times faster than expected due to human impacts. When the extinction of species culminates in functional loss, ecosystem functioning is altered. Functional extinction risk depends on taxonomic and functional rarity, with the non‐redundant traits found in rare species being the most vulnerable. To investigate the relationship between taxonomic rarity and functional extinction, we ran extinction simulations driven by taxonomic rarity. Firstly, we sampled the fish fauna of 40 pristine Amazonian streams and compiled functional traits related to the body size, defence, diet, stratification, and activity of species. Then, we removed species, beginning with the rarest and ending with the commonest (and vice‐versa) and compared the observed patterns with random extinction at local and regional scales. Following the removal of rare species, the functional rarity and body size of the community both decreased, and functional extinctions occurred after less than 10% of extinction at both spatial scales. Otherwise, the removal of common species resulted in an increase in functional rarity at the local scale, although widespread species ensured the persistence of a set of unique functional traits at a regional scale. Additionally, more than 60% of the common species had to go extinct before any functional extinction occurred at either scale. If the ongoing mass extinction targets rare species, Amazonian stream ecosystems will be impacted by the loss of fish species associated with vulnerable functions. We propose an extinction risk assessment based on the ecosystem and recommend that future studies apply our approach to other taxa and ecosystems, to better understand the effects of human impacts on ecosystem functioning.

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